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Tag Archives: Masaryk University

ToPASeq – an R package for topology-based pathway analysis of microarray and RNA-Seq data

November 4, 2015 Leave a comment 7,863 Views

rna-seq

Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses. The last generation of pathway analysis methods takes into account the topological structure ...

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TET1 promotes RXRα expression and adipogenesis through DNA demethylation
8 March 2021
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Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits
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B3GNT3 acts as a carcinogenic factor in endometrial cancer via facilitating cell growth, invasion and migration through regulating RhoA/RAC1 pathway-associated markers
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Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
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What is RNA-Seq?

long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. These three types are used to generate a base-resolution expression profile for each gene. Nat Rev Genet 10(1):57-63 (2009)


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